Supporting information formanuscript
Diverse bacteria isolated from microthermoil-production water
Ji-Quan Sun1,2*, Lian Xu1,2*, Zhao Zhang1, Yan Li1, Yue-Qin Tang1,Xiao-Lei Wu1,2**
1 College of Engineering, Peking University, Beijing 100871, PR China
2Institute of Engineering (Baotou), College of Engineering, Peking University, Baotou 014030, PRChina
*Authors contribute equally
**Corresponding author:
Xiao-Lei Wu, College of Engineering, Peking University, Beijing 100871, People’s Republic of China, Tel/Fax: +86-10-62759047. E-mail address:
Running title: Culturable bacterial strains in oil production water
Table S1Degradation characteristic of strains obtained from oil production water, strains not listed here could not degrade n-hexadecane, phenol, and phenol. “+” represents positive, “-” negative.
Strains / Phenol / n-Hexadecane / PhenanthreneActinobacteria
Dietzia sp. Cai-32 / - / + / -
Dietzia sp. Cai-40 / - / + / -
Dietzia sp. CW-21 / - / + / -
Dietzia sp. CY-b19 / - / + / -
Dietzia sp. CW-19 / - / + / -
Dietzia sp. X-b1 / - / + / -
Dietzia sp. X-c3 / - / + / -
Micrococcus sp. X-48 / - / + / -
Firmicutes
Bavariicoccus sp. CY-31 / - / + / -
Enterococcus sp. CY-29 / + / + / -
Exiguobacterium sp. CW-a3 / - / - / +
Halolactibacillus sp. CY-b31 / - / - / +
Paenibacillus sp. X-47 / - / - / +
Planococcus sp. CW-123 (=CY-a1 =Cai-18) / - / + / -
Planococcus sp. CY-b41 / - / + / -
Trichococcus sp. CY-44 / - / + / -
Alphaproteobacteria
Paracoccus sp. CY-b26 / - / + / -
Rhizobium sp. Cai-b7 / - / + / -
Rhodobacter sp. CW-39 (=CY-b45 = Cai-42) / - / + / -
Betaproteobacteria
Acidovorax sp. X-11-3 / - / + / -
Alcaligenaceae strain X-17 / - / - / +
Alcaligenes sp. X-a9 (=CY-a4) / + / - / -
Alcaligenes sp. CY-d19 / + / - / -
Comamonas sp. CY-b24 / + / - / -
Gammaproteobacteria
Acinetobacter sp. Cai-20 / - / + / -
Acinetobacter sp. Cai-b1 / +
Pseudomonas sp. Cai-b3 (= CW-a35) / - / + / +
Pseudomonas sp. CW-122 (=CY-a4) / - / + / -
Pseudomonas sp. CW-a2 (= X-b18= Cai-b2) / - / + / -
Pseudomonas sp. X-b2 / - / + / -
Table S2 The isolates with lower 16S rRNA gene similarity to known type strains and the isolates with hydrocarbon-degrading abilities
Agars / Clones / Isolates / Strains / Potential novel species (16S rRNA gene similarity<98%) / Alkane monooxygenase gene / Phenol hydroxylase gene / n-Hexadecane / Phenol-degradation / PhenanthreneNum / Rat / Num / Rat / Num / Rat / Num / Rat / Num / Rat / Num / Rat
Cai / 42 / 41 / 13 / 1 / 7.7% / 5 / 30.8% / 0 / 0 / 6 / 46.2% / 0 / 0 / 1 / 7.7%
CW / 140 / 76 / 15 / 4 / 26.7% / 4 / 26.7% / 0 / 0 / 6 / 40.0% / 0 / 0 / 2 / 13.3%
CY / 134 / 69 / 27 / 3 / 11.1% / 5 / 18.5% / 3 / 11.1% / 9 / 33.3% / 4 / 14.8% / 1 / 3.7%
X / 119 / 60 / 25 / 2 / 8.0% / 4 / 16.0% / 2 / 8.0% / 6 / 24.0% / 1 / 4.0% / 3 / 12.0%
Table S3 Degradation characteristics of isolates on n-hexadecane, phenol and phenanthrene, and the detection of functional genes
Isolate / 16S rDNA accession No. / Closest type strain / 16S rDNA similarity (%) / Degradation / GenesPhe / Hex / Phen / PH / alkB
Cai-b5 / JX997907 / Microbacterium oxydans (Y17227) / 100%
Cai-18 / JX997867 / Planococcus rifietoensis (AJ493659) / 99.61% / +
Cai-12 / JX997854 / Brevundimonas mediterranea (AJ227801) / 99.84%
Cai-39 / JX997860 / Rhizobium selenitireducens (EF440185) / 98.74% / +
Cai-2-1 / JX997864 / Rhizobium selenitireducens (EF440185) / 99.05%
Cai-b7 / JX997863 / Rhizobium selenitireducens (EF440185) / 99.21% / + / +
Cai-20 / JX997898 / Acinetobacter schindleri (AJ278311) / 99.12% / + / +
Cai-b1 / JX997899 / Acinetobacter lwoffii (X81665) / 99.70%
Cai-b2 / JX997886 / Pseudomonas stutzeri (AF094748) / 98.90% / + / +
Cai-b3 / JX997890 / Pseudomonas xanthomarina (AB176954) / 99.34% / + / +
Cai-42 / JX997851 / Rhodobacter azotoformans (D70846) / 96.24%
Cai-32 / JX997914 / Dietzia cercidiphylli (EU375846) / 100% / + / +
Cai-40 / JX997910 / Dietzia maris (X79290) / 100% / + / +
CW-a2 / JX997884 / Pseudomonas stutzeri (AF094748) / 98.90% / + / +
CW-a4 / JX997887 / Pseudomonas stutzeri (AF094748) / 98.97%
CW-122 / JX997892 / Pseudomonas agarici (Z76652) / 98.31% / +
CW-a35 / JX997891 / Pseudomonas xanthomarina (AB176954) / 99.34% / + / +
CW-a21 / JX997858 / Sphingomonas paucimobilis (U37337) / 99.69%
CW-39 / JX997849 / Rhodobacter azotoformans (D70846) / 96.24% / + / +
CW-1 / JX997862 / Rhizobium selenitireducens (EF440185) / 98.74% / +
CW-123 / JX997866 / Planococcus rifietoensis (AJ493659) / 99.61% / +
CW-19 / KC209819 / Dietzia cercidiphylli (EU375846) / 100% / + / +
CW-21 / JX997911 / Dietzia cercidiphylli (EU375846) / 100% / + / +
CW-103 / JX997905 / Sanguibacter soli (EF547937) / 97.65%
CW-44 / JX997904 / Sanguibacter soli (EF547937) / 97.25%
CW-a23 / JX997908 / Microbacterium oxydans (Y17227) / 100%
CW-a28 / JX997872 / Bacillus endophyticus (AF295302) / 94.50%
CW-a3 / JX997880 / Exiguobacterium aurantiacum (DQ019166) / 100% / +
X-18 / JX997856 / Brevundimonas mediterranea (AJ227801) / 99.84%
X-d11 / JX997846 / Comamonas aquatica (AJ430344) / 97.74%
X-a12 / JX997845 / Delftia lacustris (EU888308) / 100%
X-d2 / JX997837 / Parapusillimonas granuli (DQ466075) / 98.23%
X-b15 / JX997839 / Parapusillimonas granuli (DQ466075) / 98.23%
X-b18 / JX997885 / Pseudomonas stutzeri (AF094748) / 98.90% / + / +
X-b2 / JX997894 / Pseudomonas grimontii (AF268029) / 99.71% / +
X-a5 / JX997895 / Pseudomonas caeni (EU620679) / 99.42%
X-a8 / JX997896 / Pseudomonas caeni (EU620679) / 99.48%
X-a10 / JX997897 / Pseudomonas caeni (EU620679) / 99.63%
X-a11 / JX997900 / Shewanella baltica (AJ000214) / 99.05%
X-b11 / JX997903 / Stenotrophomonas acidaminiphila (AF273080) / 99.78%
X-a9 / JX997840 / Alcaligenes faecalis (AJ242986) / 100% / + / +
X-17 / JX997838 / Kerstersia gyiorum (AY131213) / 99.04% / +
Bordetella trematum (AJ277798) / 99.04%
X-11 / JX997843 / Acidovorax facilis (AF078765) / 99.52%
X-11-3 / JX997844 / Acidovorax facilis (AF078765) / 98.56% / +
X-b4 / JX997857 / Sphingobium xenophagum (X94098) / 99.13% / +
X-b17 / JX997859 / Rhizobium selenitireducens (EF440185) / 98.74% / +
X-47 / JX997883 / Paenibacillus ehimensis (AY116665) / 99.06% / +
X-d1 / JX997881 / Paenibacillus ehimensis (AY116665) / 99.85%
X-48 / JX997909 / Micrococcus flavus (DQ491453) / 99.40% / +
X-b1 / KC209818 / Dietzia cercidiphylli (EU375846) / 100% / +
X-c3 / JX997913 / Dietzia cercidiphylli (EU375846) / 100% / +
X-d4 / JX997906 / Cellulosimicrobium funkei (AY501364) / 99.84% / +
X-d8 / JX997882 / Erysipelothrix rhusiopathiae (AB034200) / 95.03%
CY-b6 / JX997901 / Shewanella baltica (AJ000214) / 98.16%
CY-b25 / JX997902 / Stenotrophomonas acidaminiphila (AF273080) / 99.78%
CY-b36 / JX997888 / Pseudomonas stutzeri (AF094748) / 98.90%
CY-b40 / JX997889 / Pseudomonas stutzeri (AF094748) / 100%
CY-a4 / JX997893 / Pseudomonas agarici (Z76652) / 98.24% / +
CY-b24 / JX997847 / Comamonas testosteroni (M11224) / 100% / + / +
CY-63 / JX997848 / Parapusillimonas granuli (DQ466075) / 98.23%
CY-a4 / JX997841 / Alcaligenes faecalis (AJ242986) / 100% / +
CY-d19 / JX997842 / Alcaligenes faecalis (AJ242986) / 100% / + / +
CY-b45 / JX997850 / Rhodobacter azotoformans (D70846) / 96.24%
CY-b35 / JX997861 / Rhizobium selenitireducens (EF440185) / 98.74% / +
CY-b26 / JX997852 / Paracoccus kondratievae (AF250332) / 98.58% / + / +
CY-b28 / JX997853 / Paracoccus denitrificans (Y16927) / 100%
CY-33 / JX997855 / Brevundimonas mediterranea (AJ227801) / 99.84%
CY-a1 / JX997865 / Planococcus rifietoensis (AJ493659) / 99.61% / +
CY-b29 / JX997868 / Planococcus maritimus (AF500007) / 99.45%
CY-b41 / JX997869 / Planococcus donghaensis (EF079063) / 99.30% / +
CY-b27 / JX997870 / Planomicrobium flavidum (FJ265708) / 98.89%
CY-b32 / JX997874 / Trichococcus patagoniensis (AF394926) / 100%
CY-44 / JX997875 / Trichococcus palustris (AJ296179) / 96.58% / + / +
CY-b31 / JX997873 / Halolactibacillus halophilus (AB196783) / 98.90% / +
CY-16 / JX997877 / Enterococcus casseliflavus (AF039903) / 100% / +
CY-29 / JX997878 / Enterococcus saccharolyticus (AF061004) / 98.91% / + / + / +
CY-31 / JX997876 / Bavariicoccus seileri (FM177901) / 100% / + / +
CY-87 / JX997879 / Enterococcus saccharolyticus (AF061004) / 98.83%
CY-90 / JX997916 / Arcanobacterium hippocoleae (AJ300767) / 93.51%
CY-b19 / JX997912 / Dietzia cercidiphylli (EU375846) / 100% / + / +
CY-b33 / JX997871 / Bacillus thuringiensis (AF290545) / 99.69%
Fig.S1 the curves of bacterial clones emerged on the different agars at different time points
Fig.S2Phylogenetic tree based on partial sequence of 16S rRNA gene from Actinobacteriaphylum strains was constructed by the neighbor-joining method. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.01 substitutions per site. The tree topology was evaluated with the maximum-likelihood and maximum-parsimony algorithms.
Fig.S3Phylogenetic tree based on partial sequence of 16S rRNA gene from Firmicutes phylum strains was constructed by the neighbor-joining method. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.02 substitutions per site. The tree topology was evaluated with the maximum-likelihood and maximum-parsimony algorithms.
Fig.S4Phylogenetic tree based on partial sequence of 16S rRNA gene from Alphaproteobacteriaorder strains was constructed by the neighbor-joining method. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.01 substitutions per site. The tree topology was evaluated with the maximum-likelihood and maximum-parsimony algorithms
Fig.S5Phylogenetic tree based on partial sequence of 16S rRNA gene from Betaproteobacteriaorder strains was constructed by the neighbor-joining method. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.01 substitutions per site. The tree topology was evaluated with the maximum-likelihood and maximum-parsimony algorithms.
Fig.S6Phylogenetic tree based on partial sequence of 16S rRNA gene from Gammaproteobacteriaorder strains was constructed by the neighbor-joining method. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.01 substitutions per site. The tree topology was evaluated with the maximum-likelihood and maximum-parsimony algorithms.
Fig.S7Phylogenetic tree based on the partial Phenol hydroxylase gene was constructed by the neighbor-joining method. Tree topology was evaluated by bootstrap analysis based on 1000 resampling replicates with the MEGA software package version 5.0. Bootstrap values (%) are indicated at the nodes (only greater than 50% were shown). The scale bars represent 0.02 substitutions per site.All of these strains listed here were type strains, except the strains obtained in this study